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Gene (snp-normalizer)
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de.hu.berlin.wbi.objects</FONT>
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Class Gene</H2>
<PRE>
<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
  <IMG SRC="../../../../../resources/inherit.gif" ALT="extended by "><B>de.hu.berlin.wbi.objects.Gene</B>
</PRE>
<DL>
<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../de/hu/berlin/wbi/psb/GenePSB.html" title="class in de.hu.berlin.wbi.psb">GenePSB</A></DD>
</DL>
<HR>
<DL>
<DT><PRE>public class <B>Gene</B><DT>extends <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>
</PRE>

<P>
Represents a gene mention found by any Named Enttiy Recognition and Normalization tool. 
 In this work we always used GNAT and gene2pubmed
<P>

<P>
<DL>
<DT><B>Author:</B></DT>
  <DD>Philippe Thomas</DD>
</DL>
<HR>

<P>

<!-- ======== CONSTRUCTOR SUMMARY ======== -->

<A NAME="constructor_summary"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#Gene()">Gene</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Empty constructor</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#Gene(int, int, int, int, de.hu.berlin.wbi.objects.EntityOffset, java.lang.String)">Gene</A></B>(int&nbsp;pmid,
     int&nbsp;geneID,
     int&nbsp;confidence,
     int&nbsp;species,
     <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location,
     <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;entity)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
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&nbsp;
<!-- ========== METHOD SUMMARY =========== -->

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<B>Method Summary</B></FONT></TH>
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<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(non-Javadoc)</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#getConfidence()">getConfidence</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the confidence for this gene.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#getEntity()">getEntity</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the string in the text.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#getGeneID()">getGeneID</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the gene-ID (Entrez in our case).</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#getLocation()">getLocation</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the found at which position.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#getPmid()">getPmid</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the article ID.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#getSpecies()">getSpecies</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the species.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#hashCode()">hashCode</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(non-Javadoc)</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>static&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#init(de.hu.berlin.wbi.objects.DatabaseConnection, java.lang.String, java.lang.String)">init</A></B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>&nbsp;mysql,
     <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;geneTable,
     <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;gene2Pubmed)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Initializes the prepared statements</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>static&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>&gt;</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#queryGenesForArticle(int)">queryGenesForArticle</A></B>(int&nbsp;pmid)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Search for all genes contained in an Article using PubMed ID.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html#toString()">toString</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(non-Javadoc)</TD>
</TR>
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<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
</TR>
</TABLE>
&nbsp;
<P>

<!-- ========= CONSTRUCTOR DETAIL ======== -->

<A NAME="constructor_detail"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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<B>Constructor Detail</B></FONT></TH>
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<A NAME="Gene()"><!-- --></A><H3>
Gene</H3>
<PRE>
public <B>Gene</B>()</PRE>
<DL>
<DD>Empty constructor
<P>
</DL>
<HR>

<A NAME="Gene(int, int, int, int, de.hu.berlin.wbi.objects.EntityOffset, java.lang.String)"><!-- --></A><H3>
Gene</H3>
<PRE>
public <B>Gene</B>(int&nbsp;pmid,
            int&nbsp;geneID,
            int&nbsp;confidence,
            int&nbsp;species,
            <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location,
            <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;entity)</PRE>
<DL>
<DL>
<DT><B>Parameters:</B><DD><CODE>pmid</CODE> - <DD><CODE>geneID</CODE> - <DD><CODE>confidence</CODE> - <DD><CODE>species</CODE> - <DD><CODE>location</CODE> - <DD><CODE>entity</CODE> - </DL>
</DL>

<!-- ============ METHOD DETAIL ========== -->

<A NAME="method_detail"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
<B>Method Detail</B></FONT></TH>
</TR>
</TABLE>

<A NAME="getPmid()"><!-- --></A><H3>
getPmid</H3>
<PRE>
public int <B>getPmid</B>()</PRE>
<DL>
<DD>Gets the article ID.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the article ID</DL>
</DD>
</DL>
<HR>

<A NAME="getGeneID()"><!-- --></A><H3>
getGeneID</H3>
<PRE>
public int <B>getGeneID</B>()</PRE>
<DL>
<DD>Gets the gene-ID (Entrez in our case).
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the gene-ID (Entrez in our case)</DL>
</DD>
</DL>
<HR>

<A NAME="getConfidence()"><!-- --></A><H3>
getConfidence</H3>
<PRE>
public int <B>getConfidence</B>()</PRE>
<DL>
<DD>Gets the confidence for this gene.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the confidence for this gene</DL>
</DD>
</DL>
<HR>

<A NAME="getSpecies()"><!-- --></A><H3>
getSpecies</H3>
<PRE>
public int <B>getSpecies</B>()</PRE>
<DL>
<DD>Gets the species.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the species</DL>
</DD>
</DL>
<HR>

<A NAME="getLocation()"><!-- --></A><H3>
getLocation</H3>
<PRE>
public <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A> <B>getLocation</B>()</PRE>
<DL>
<DD>Gets the found at which position.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the found at which position</DL>
</DD>
</DL>
<HR>

<A NAME="getEntity()"><!-- --></A><H3>
getEntity</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getEntity</B>()</PRE>
<DL>
<DD>Gets the string in the text.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the string in the text</DL>
</DD>
</DL>
<HR>

<A NAME="toString()"><!-- --></A><H3>
toString</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>
<DL>
<DD>(non-Javadoc)
<P>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>See Also:</B><DD><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang"><CODE>Object.toString()</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="hashCode()"><!-- --></A><H3>
hashCode</H3>
<PRE>
public int <B>hashCode</B>()</PRE>
<DL>
<DD>(non-Javadoc)
<P>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>See Also:</B><DD><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang"><CODE>Object.hashCode()</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="equals(java.lang.Object)"><!-- --></A><H3>
equals</H3>
<PRE>
public boolean <B>equals</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</PRE>
<DL>
<DD>(non-Javadoc)
<P>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>See Also:</B><DD><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang"><CODE>Object.equals(java.lang.Object)</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="init(de.hu.berlin.wbi.objects.DatabaseConnection, java.lang.String, java.lang.String)"><!-- --></A><H3>
init</H3>
<PRE>
public static void <B>init</B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A>&nbsp;mysql,
                        <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;geneTable,
                        <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;gene2Pubmed)
                 throws <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/sql/SQLException.html?is-external=true" title="class or interface in java.sql">SQLException</A></PRE>
<DL>
<DD>Initializes the prepared statements
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>mysql</CODE> - <DD><CODE>geneTable</CODE> - 
<DT><B>Throws:</B>
<DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/sql/SQLException.html?is-external=true" title="class or interface in java.sql">SQLException</A></CODE></DL>
</DD>
</DL>
<HR>

<A NAME="queryGenesForArticle(int)"><!-- --></A><H3>
queryGenesForArticle</H3>
<PRE>
public static <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A>&gt; <B>queryGenesForArticle</B>(int&nbsp;pmid)</PRE>
<DL>
<DD>Search for all genes contained in an Article using PubMed ID.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>pmid</CODE> - PubMed-ID
<DT><B>Returns:</B><DD>all genes contained in a specific article</DL>
</DD>
</DL>
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